=>> Building science/py-MDAnalysis build started at Tue Jul 7 18:46:42 JST 2026 port directory: /usr/ports/science/py-MDAnalysis package name: py312-MDAnalysis-2.10.0_1 building for: FreeBSD s15amd64-setuptools2-job-07 15.1-STABLE FreeBSD 15.1-STABLE 1501501 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1551 Jul 5 18:52 /usr/ports/science/py-MDAnalysis/Makefile Ports top last git commit: 18628b9022c9c1c0e7cb5e71c2aa1e1e563ca34a Ports top unclean checkout: yes Port dir last git commit: 724850426e4d8acc06c5ce8827e69d705b163609 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.8 Host OSVERSION: 1501501 Jail OSVERSION: 1501501 Job Id: 07 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1501501 UNAME_v=FreeBSD 15.1-STABLE 1501501 UNAME_r=15.1-STABLE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 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DOCSDIR=/usr/local/share/doc/MDAnalysis EXAMPLESDIR=/usr/local/share/examples/MDAnalysis WWWDIR=/usr/local/www/MDAnalysis ETCDIR=/usr/local/etc/MDAnalysis --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles OVERLAYS+=/overlays/overlay_setuptools FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### LICENSES_ACCEPTED= EULA ISC MPEG2ENC DEFAULT_VERSIONS+= magick=7 DEFAULT_VERSIONS+= pgsql=18 DEFAULT_VERSIONS+= samba=4.23 DEFAULT_VERSIONS+= ssl=openssl japanese_fcitx5-mozc_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_UNSET= JAWIKI x11_wm_hikari_SET= INPUTMETHOD GAMMA LAYERSHELL SCREENCOPY VIRTUALINPUT X11 .if $(.CURDIR:M*/x11-wm/hikari) WITH_DEBUG= YES .endif #### #### devel_gamin_set= LIBINOTIFY #### Misc Poudriere #### .include "/etc/make.conf.ports_env" DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (kbytes, -y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License GPLv2 accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py312-MDAnalysis-2.10.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.7.5.pkg [s15amd64-setuptools2-job-07] Installing pkg-2.7.5... [s15amd64-setuptools2-job-07] Extracting pkg-2.7.5: .......... done ===> py312-MDAnalysis-2.10.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py312-MDAnalysis-2.10.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv2 accepted by the user => mdanalysis-2.10.0.tar.gz doesn't seem to exist in /portdistfiles. => Attempting to fetch https://files.pythonhosted.org/packages/source/m/mdanalysis/mdanalysis-2.10.0.tar.gz mdanalysis-2.10.0.tar.gz 5139 kB 60 MBps 00s ===> Fetching all distfiles required by py312-MDAnalysis-2.10.0_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by py312-MDAnalysis-2.10.0_1 for building => SHA256 Checksum OK for mdanalysis-2.10.0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by py312-MDAnalysis-2.10.0_1 for building ===> Extracting for py312-MDAnalysis-2.10.0_1 => SHA256 Checksum OK for mdanalysis-2.10.0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Patching for py312-MDAnalysis-2.10.0_1 ===> Applying FreeBSD patches for py312-MDAnalysis-2.10.0_1 from /usr/ports/science/py-MDAnalysis/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py312-MDAnalysis-2.10.0_1 depends on package: py312-numpy>=1.26.0 - not found ===> Installing existing package /packages/All/py312-numpy-2.4.6_1,1.pkg [s15amd64-setuptools2-job-07] Installing py312-numpy-2.4.6_1,1... 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[s15amd64-setuptools2-job-07] | `-- Extracting mpdecimal-4.0.1: .......... done [s15amd64-setuptools2-job-07] | `-- Installing openssl-3.0.21,1... [s15amd64-setuptools2-job-07] | `-- Extracting openssl-3.0.21,1: .......... done [s15amd64-setuptools2-job-07] | `-- Installing readline-8.3.3... [s15amd64-setuptools2-job-07] | `-- Extracting readline-8.3.3: .......... done [s15amd64-setuptools2-job-07] `-- Extracting python312-3.12.13_3: .......... done [s15amd64-setuptools2-job-07] Extracting py312-numpy-2.4.6_1,1: .......... done ===== Message from gcc14-14.2.0_6: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc14 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===== Message from openssl-3.0.21,1: -- This port (security/openssl) will update from 3.0 to 3.5 per 2026-07-01 (2026Q3) in anticipation of the End-of-Life of OpenSSL 3.0. A new port (security/openssl30) will be created for the remainder of the lifespan of OpenSSL 3.0 and FreeBSD 14. See: https://openssl-library.org/roadmap/index.html ===== Message from python312-3.12.13_3: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py312-gdbm databases/py-gdbm@py312 py312-sqlite3 databases/py-sqlite3@py312 py312-tkinter x11-toolkits/py-tkinter@py312 ===> py312-MDAnalysis-2.10.0_1 depends on package: py312-numpy>=1.26.0 - found ===> Returning to build of py312-MDAnalysis-2.10.0_1 ===> py312-MDAnalysis-2.10.0_1 depends on package: py312-packaging>=2.0 - not found ===> Installing existing package /packages/All/py312-packaging-26.2.pkg [s15amd64-setuptools2-job-07] Installing py312-packaging-26.2... [s15amd64-setuptools2-job-07] Extracting py312-packaging-26.2: .......... done ===> py312-MDAnalysis-2.10.0_1 depends on package: py312-packaging>=2.0 - found ===> Returning to build of py312-MDAnalysis-2.10.0_1 ===> py312-MDAnalysis-2.10.0_1 depends on package: py312-cython>=3.2.4 - not found ===> Installing existing package /packages/All/py312-cython-3.2.4.pkg [s15amd64-setuptools2-job-07] Installing py312-cython-3.2.4... [s15amd64-setuptools2-job-07] Extracting py312-cython-3.2.4: .......... done ===> py312-MDAnalysis-2.10.0_1 depends on package: py312-cython>=3.2.4 - found ===> Returning to build of py312-MDAnalysis-2.10.0_1 ===> py312-MDAnalysis-2.10.0_1 depends on package: py312-setuptools>=63.1.0 - not found ===> Installing existing package /packages/All/py312-setuptools-81.0.0.pkg [s15amd64-setuptools2-job-07] Installing py312-setuptools-81.0.0... [s15amd64-setuptools2-job-07] `-- Installing py312-more-itertools-11.1.0... 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[s15amd64-setuptools2-job-07] `-- Extracting py312-wheel-0.47.0: .......... done [s15amd64-setuptools2-job-07] Extracting py312-setuptools-81.0.0: .......... done ===> py312-MDAnalysis-2.10.0_1 depends on package: py312-setuptools>=63.1.0 - found ===> Returning to build of py312-MDAnalysis-2.10.0_1 ===> py312-MDAnalysis-2.10.0_1 depends on file: /usr/local/bin/python3.12 - found =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for py312-MDAnalysis-2.10.0_1 performance hint: MDAnalysis/lib/c_distances.pyx:273:0: Exception check on '_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:300:0: Exception check on '_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:390:37: Exception check after calling '__pyx_fuse_0_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_0_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_0_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:390:37: Exception check after calling '__pyx_fuse_1_minimum_image_orthogonal' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_1_minimum_image_orthogonal' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_1_minimum_image_orthogonal' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:414:36: Exception check after calling '__pyx_fuse_0_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_0_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_0_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/c_distances.pyx:414:36: Exception check after calling '__pyx_fuse_1_minimum_image_triclinic' will always require the GIL to be acquired. Possible solutions: 1. Declare '__pyx_fuse_1_minimum_image_triclinic' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on '__pyx_fuse_1_minimum_image_triclinic' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:417:37: Exception check after calling 'coord2cellid' will always require the GIL to be acquired. Declare 'coord2cellid' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:431:26: Exception check after calling 'coord2cellxyz' will always require the GIL to be acquired. Possible solutions: 1. Declare 'coord2cellxyz' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'coord2cellxyz' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:559:34: Exception check after calling 'coord2cellxyz' will always require the GIL to be acquired. Possible solutions: 1. Declare 'coord2cellxyz' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'coord2cellxyz' to allow an error code to be returned. performance hint: MDAnalysis/lib/nsgrid.pyx:567:56: Exception check after calling 'cellxyz2cellid' will always require the GIL to be acquired. Declare 'cellxyz2cellid' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:574:53: Exception check after calling 'calc_distsq' will always require the GIL to be acquired. Declare 'calc_distsq' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. performance hint: MDAnalysis/lib/nsgrid.pyx:578:57: Exception check after calling 'add_neighbors' will always require the GIL to be acquired. Possible solutions: 1. Declare 'add_neighbors' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'add_neighbors' to allow an error code to be returned. Attempting to autodetect OpenMP support... Compiler supports OpenMP Will attempt to use Cython. Compiling MDAnalysis/lib/formats/libdcd.pyx because it changed. Compiling MDAnalysis/lib/c_distances.pyx because it changed. Compiling MDAnalysis/lib/c_distances_openmp.pyx because it changed. Compiling MDAnalysis/lib/qcprot.pyx because it changed. Compiling MDAnalysis/lib/formats/libmdaxdr.pyx because it changed. Compiling MDAnalysis/lib/formats/cython_util.pyx because it changed. Compiling MDAnalysis/analysis/encore/cutils.pyx because it changed. Compiling MDAnalysis/analysis/encore/clustering/affinityprop.pyx because it changed. Compiling MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx because it changed. Compiling MDAnalysis/lib/_cutil.pyx because it changed. Compiling MDAnalysis/lib/_augment.pyx because it changed. Compiling MDAnalysis/lib/nsgrid.pyx because it changed. Compiling MDAnalysis/coordinates/timestep.pyx because it changed. [ 1/13] Cythonizing MDAnalysis/analysis/encore/clustering/affinityprop.pyx [ 2/13] Cythonizing MDAnalysis/analysis/encore/cutils.pyx [ 3/13] Cythonizing MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx [ 4/13] Cythonizing MDAnalysis/coordinates/timestep.pyx [ 5/13] Cythonizing MDAnalysis/lib/_augment.pyx [ 6/13] Cythonizing MDAnalysis/lib/_cutil.pyx [ 7/13] Cythonizing MDAnalysis/lib/c_distances.pyx [ 8/13] Cythonizing MDAnalysis/lib/c_distances_openmp.pyx [ 9/13] Cythonizing MDAnalysis/lib/formats/cython_util.pyx [10/13] Cythonizing MDAnalysis/lib/formats/libdcd.pyx [11/13] Cythonizing MDAnalysis/lib/formats/libmdaxdr.pyx [12/13] Cythonizing MDAnalysis/lib/nsgrid.pyx [13/13] Cythonizing MDAnalysis/lib/qcprot.pyx /usr/local/lib/python3.12/site-packages/setuptools/_distutils/dist.py:287: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/local/lib/python3.12/site-packages/setuptools/_distutils/dist.py:287: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /usr/local/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2027-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) /usr/local/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! dist._finalize_license_expression() /usr/local/lib/python3.12/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running config =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for py312-MDAnalysis-2.10.0_1 Attempting to autodetect OpenMP support... Compiler supports OpenMP Will attempt to use Cython. /usr/local/lib/python3.12/site-packages/setuptools/_distutils/dist.py:287: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/local/lib/python3.12/site-packages/setuptools/_distutils/dist.py:287: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /usr/local/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2027-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) /usr/local/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! dist._finalize_license_expression() /usr/local/lib/python3.12/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis copying MDAnalysis/due.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis copying MDAnalysis/authors.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis copying MDAnalysis/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis copying MDAnalysis/version.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis copying MDAnalysis/exceptions.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis copying MDAnalysis/units.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/contacts.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/backends.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/dielectric.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/polymer.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/waterdynamics.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/psa.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/diffusionmap.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/rdf.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/lineardensity.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/base.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/density.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/distances.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/helix_analysis.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/results.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/bat.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/msd.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/align.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/gnm.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/nuclinfo.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/nucleicacids.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/rms.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/leaflet.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/dihedrals.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/pca.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis copying MDAnalysis/analysis/atomicdistances.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/tests copying MDAnalysis/tests/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/tests copying MDAnalysis/tests/datafiles.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/tests creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/pkdtree.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/log.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/distances.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_distopia.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/transformations.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/mdamath.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/util.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/picklable_file_io.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/NeighborSearch.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/correlations.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/core copying MDAnalysis/core/topology.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/core copying MDAnalysis/core/topologyobjects.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/core copying MDAnalysis/core/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/core copying MDAnalysis/core/_get_readers.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/core copying MDAnalysis/core/selection.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/core copying MDAnalysis/core/topologyattrs.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/core copying MDAnalysis/core/accessors.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/core copying MDAnalysis/core/groups.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/core copying MDAnalysis/core/universe.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/core creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/guesser copying MDAnalysis/guesser/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/guesser copying MDAnalysis/guesser/base.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/guesser copying MDAnalysis/guesser/tables.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/guesser copying MDAnalysis/guesser/default_guesser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/guesser creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/nojump.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/base.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/positionaveraging.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/fit.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/boxdimensions.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/translate.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/rotate.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/transformations copying MDAnalysis/transformations/wrap.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/transformations creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/PSFParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/GSDParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/DLPolyParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/XYZParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/PDBQTParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/MinimalParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/TPRParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/base.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/GMSParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/CRDParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/PQRParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/guessers.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/tables.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/TOPParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/PDBParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/ParmEdParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/MMTFParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/MOL2Parser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/GROParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/core.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/TXYZParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/ITPParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology copying MDAnalysis/topology/DMSParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/visualization copying MDAnalysis/visualization/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/visualization copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/visualization creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/jmol.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/base.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/pymol.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/vmd.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/gromacs.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/selections copying MDAnalysis/selections/charmm.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/selections creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/IMD.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/null.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/H5MD.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/DCD.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/XTC.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/MOL2.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/MMTF.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/memory.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/chain.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TPR.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/DMS.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/GRO.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/base.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/ParmEd.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/DLPoly.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/CRD.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDBQT.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TNG.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/GSD.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/GMS.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/INPCRD.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/PDB.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/chemfiles.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRJ.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/XDR.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRR.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/core.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TXYZ.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRZ.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/PQR.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/TRC.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/XYZ.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/RDKitParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/RDKitInferring.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/OpenMMParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/base.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/ParmEd.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/OpenMM.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/RDKit.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/converters copying MDAnalysis/converters/ParmEdParser.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/converters creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/base.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/XVG.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/core.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/auxiliary copying MDAnalysis/auxiliary/EDR.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/auxiliary creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/legacy copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/legacy creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/similarity.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/covariance.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/utils.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/hbonds copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/hbonds creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/hole2 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/hole2 creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/dssp copying MDAnalysis/analysis/dssp/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/dssp copying MDAnalysis/analysis/dssp/dssp.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/dssp copying MDAnalysis/analysis/dssp/pydssp_numpy.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/dssp creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/filenames.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/data creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/hydrogenbonds copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/hydrogenbonds creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/clustering creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/include copying MDAnalysis/lib/include/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/include creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/libmdanalysis copying MDAnalysis/lib/libmdanalysis/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/libmdanalysis creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/include creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/src creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/src/transformations creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/obj.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/utils.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology/tpr copying MDAnalysis/topology/tpr/setting.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/topology/tpr creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source copying doc/sphinx/source/conf.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source running egg_info writing MDAnalysis.egg-info/PKG-INFO writing dependency_links to MDAnalysis.egg-info/dependency_links.txt writing requirements to MDAnalysis.egg-info/requires.txt writing top-level names to MDAnalysis.egg-info/top_level.txt dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/analysis/encore/clustering/include/ap.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/include/calc_distances.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/local/lib/python3.12/site-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file 'MDAnalysis.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching 'doc/html/html' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.pyd' found anywhere in distribution warning: no previously-included files matching '*~' found anywhere in distribution warning: no previously-included files matching '.git' found anywhere in distribution adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/data copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/data copying doc/README -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc copying MDAnalysis/lib/_augment.cpp -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_augment.pyx -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_cutil.cpp -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pxd -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/_cutil.pyx -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances.c -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pxd -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances.pyx -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.cpp -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/nsgrid.pyx -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/qcprot.c -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/lib/qcprot.pyx -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib copying MDAnalysis/coordinates/timestep.cpp -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pxd -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/coordinates/timestep.pyx -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/coordinates copying MDAnalysis/analysis/encore/cutils.c -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/clustering copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/clustering creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/include copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/include creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/dimensionality_reduction/src creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/clustering/include copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/clustering/include creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/clustering/src copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/analysis/encore/clustering/src copying MDAnalysis/lib/include/calc_distances.h -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/include copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/libmdanalysis copying MDAnalysis/lib/formats/cython_util.c -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.c -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/include copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/src copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/src/transformations copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/src/transformations copying doc/sphinx/Makefile -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx copying doc/sphinx/source/index.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source copying doc/sphinx/source/references.bib -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/analysis_modules.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/auxiliary_modules.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/converters.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/coordinates_modules.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/core_modules.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/exceptions.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/guesser_modules.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/lib_modules.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/overview.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/references.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/selections.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/selections_modules.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/topology.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/topology_modules.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/trajectory_transformations.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/units.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/version.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages copying doc/sphinx/source/documentation_pages/visualization_modules.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/images copying doc/sphinx/source/images/AnalysisBase_parallel.png -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/images copying doc/sphinx/source/images/RSMD_plot.png -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/images copying doc/sphinx/source/images/janin_demo_plot.png -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/images copying doc/sphinx/source/images/janin_ref_plot.png -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/images copying doc/sphinx/source/images/msd_demo_plot.png -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/images copying doc/sphinx/source/images/parallelization_time.png -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/images copying doc/sphinx/source/images/rama_demo_plot.png -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/images copying doc/sphinx/source/images/rama_ref_plot.png -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/images creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/align.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/atomicdistances.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/backends.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/base.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/bat.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/contacts.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/data.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/density.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/dielectric.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/diffusionmap.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/dihedrals.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/distances.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/dssp.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/encore.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/gnm.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hbond_autocorrel_deprecated.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/helix_analysis.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hole2.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/hydrogenbonds.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/leaflet.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/legacy_modules.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/lineardensity.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/msd.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/nucleicacids.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/nuclinfo.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/parallelization.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/pca.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/polymer.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/psa.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/rdf.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/results.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/rms.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/waterdynamics.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis copying doc/sphinx/source/documentation_pages/analysis/wbridge_analysis.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/NeighborSearch.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/c_distances.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/c_distances_openmp.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/correlations.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/distances.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/log.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/mdamath.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/nsgrid.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/picklable_file_io.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/pkdtree.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/qcprot.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/transformations.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/lib copying doc/sphinx/source/documentation_pages/lib/util.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/lib creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/accessors.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/groups.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/init.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/selection.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/topology.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/topologyattrs.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/topologyobjects.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/core copying doc/sphinx/source/documentation_pages/core/universe.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/core creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/base.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/boxdimensions.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/fit.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/nojump.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/positionaveraging.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/rotate.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/translate.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/transformations copying doc/sphinx/source/documentation_pages/transformations/wrap.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/transformations creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/CRDParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/DLPolyParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/DMSParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/ExtendedPDBParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/FHIAIMSParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/GMSParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/GROParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/GSDParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/HoomdXMLParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/ITPParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/LAMMPSParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/MMTFParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/MOL2Parser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/MinimalParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PDBParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PDBQTParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PQRParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/PSFParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/TOPParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/TPRParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/TXYZParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/XYZParser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/base.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/core.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/guessers.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/init.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/tables.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology copying doc/sphinx/source/documentation_pages/topology/tpr_util.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/topology creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/base.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/default_guesser.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/init.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/guesser_modules copying doc/sphinx/source/documentation_pages/guesser_modules/tables.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/guesser_modules creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/streamlines.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/streamlines_3D.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/test_streamplot_3D.png -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/visualization copying doc/sphinx/source/documentation_pages/visualization/testing_streamline.png -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/visualization creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/base.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/charmm.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/gromacs.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/jmol.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/pymol.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/selections copying doc/sphinx/source/documentation_pages/selections/vmd.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/selections creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/CRD.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DCD.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DLPoly.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/DMS.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/FHIAIMS.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/GMS.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/GRO.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/GSD.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/H5MD.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/IMD.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/INPCRD.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/LAMMPS.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/MMTF.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/MOL2.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/NAMDBIN.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PDB.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PDBQT.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/PQR.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TNG.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TPR.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRC.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRJ.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRR.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TRZ.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/TXYZ.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XDR.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XTC.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/XYZ.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/base.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/chain.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/chemfiles.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/core.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/init.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/memory.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/null.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/pickle_readers.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates copying doc/sphinx/source/documentation_pages/coordinates/timestep.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/coordinates creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/OpenMM.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/ParmEd.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/RDKit.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/converters copying doc/sphinx/source/documentation_pages/converters/base.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/converters creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/EDR.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/XVG.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/base.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/core.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/auxiliary copying doc/sphinx/source/documentation_pages/auxiliary/init.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/auxiliary creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis/legacy copying doc/sphinx/source/documentation_pages/analysis/legacy/x3dna.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis/legacy creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/bootstrap.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/clustering.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/confdistmatrix.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/covariance.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/dimensionality_reduction.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/similarity.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis/encore copying doc/sphinx/source/documentation_pages/analysis/encore/utils.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/analysis/encore creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/lib/formats copying doc/sphinx/source/documentation_pages/lib/formats/libdcd.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/lib/formats copying doc/sphinx/source/documentation_pages/lib/formats/libmdaxdr.rst -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/doc/sphinx/source/documentation_pages/lib/formats running build_ext building 'MDAnalysis.lib.formats.libdcd' extension creating build/temp.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/formats/include -I/usr/local/include/python3.12 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/libdcd.o -std=c11 -O3 -funroll-loops -fsigned-zeros cc -shared -s -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/libdcd.o -L/usr/local/lib -o build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/libdcd.cpython-312.so building 'MDAnalysis.lib.c_distances' extension cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/include -I/usr/local/include/python3.12 -c MDAnalysis/lib/c_distances.c -o build/temp.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/c_distances.o -std=c11 -O3 -funroll-loops -fsigned-zeros cc -shared -s -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/c_distances.o -L/usr/local/lib -lm -o build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/c_distances.cpython-312.so building 'MDAnalysis.lib.c_distances_openmp' extension cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -DPARALLEL -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/include -I/usr/local/include/python3.12 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c11 -O3 -funroll-loops -fsigned-zeros cc -shared -s -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/c_distances_openmp.o -L/usr/local/lib -lm -lgomp -o build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/c_distances_openmp.cpython-312.so -fopenmp building 'MDAnalysis.lib.qcprot' extension cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -I/usr/local/include/python3.12 -c MDAnalysis/lib/qcprot.c -o build/temp.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/qcprot.o -std=c11 -O3 -funroll-loops -fsigned-zeros cc -shared -s -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/qcprot.o -L/usr/local/lib -o build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/qcprot.cpython-312.so building 'MDAnalysis.lib._transformations' extension creating build/temp.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/src/transformations cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -I/usr/local/include/python3.12 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/src/transformations/transformations.o -std=c11 -O3 -funroll-loops -fsigned-zeros cc -shared -s -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/src/transformations/transformations.o -L/usr/local/lib -lm -o build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/_transformations.cpython-312.so building 'MDAnalysis.lib.formats.libmdaxdr' extension creating build/temp.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/src cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/formats/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/include/python3.12 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/libmdaxdr.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/libmdaxdr.c:1186: MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from MDAnalysis/lib/formats/libmdaxdr.c:1187: MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: '/*' within block comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from MDAnalysis/lib/formats/libmdaxdr.c:1188: MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: '/*' within block comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ 3 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/formats/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/include/python3.12 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/src/trr_seek.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/src/trr_seek.c:30: /wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ In file included from MDAnalysis/lib/formats/src/trr_seek.c:31: /wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: '/*' within block comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ 2 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/formats/include -I/wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/formats -I/usr/local/include/python3.12 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.freebsd-15.1-STABLE-amd64-cpython-312/MDAnalysis/lib/formats/src/xdrfile.o -std=c11 -O3 -funroll-loops -fsigned-zeros In file included from MDAnalysis/lib/formats/src/xdrfile.c:62: /wrkdirs/usr/ports/science/py-MDAnalysis/work-py312/mdanalysis-2.10.0/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: '/*' within block comment [-Wcomment] 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- | ^ MDAnalysis/lib/formats/src/xdrfile.c:1109:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1109 | (float)maxint[2] - (float)minint[2] >= INT_MAX-2) { | ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1108:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1108 | (float)maxint[1] - (float)minint[1] >= INT_MAX-2 || | ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1107:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1107 | if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 || | ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1596:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1596 | (float)maxint[2] - (float)minint[2] >= INT_MAX-2) { | ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1595:49: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1595 | (float)maxint[1] - (float)minint[1] >= INT_MAX-2 || | ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:1594:52: warning: implicit conversion from 'int' to 'float' changes value from 2147483645 to 2147483648 [-Wimplicit-const-int-float-conversion] 1594 | if ((float)maxint[0] - (float)minint[0] >= INT_MAX-2 || | ~~ ~~~~~~~^~ MDAnalysis/lib/formats/src/xdrfile.c:2536:3: error: incompatible function pointer types initializing 'off_t (*)(XDR *, off_t, int)' (aka 'long (*)(struct XDR *, long, int)') with an expression of type 'int (XDR *, int64_t, int)' (aka 'int (struct XDR *, long, int)') [-Wincompatible-function-pointer-types] 2536 | xdrstdio_setpos, /* set offset in the stream */ | ^~~~~~~~~~~~~~~ 7 warnings and 1 error generated. error: command '/usr/bin/cc' failed with exit code 1 *** Error code 1 Stop. make: stopped making "build" in /usr/ports/science/py-MDAnalysis =>> Cleaning up wrkdir ===> Cleaning for py312-MDAnalysis-2.10.0_1 build of science/py-MDAnalysis@py312 | py312-MDAnalysis-2.10.0_1 ended at Tue Jul 7 18:48:37 JST 2026 build time: 00:02:49 !!! build failure encountered !!!